On the baseboard, we used I2C GPIO Expander (with 16 GPIOs) called PCA9535BS (see schematic, page 14). It is quite simple to connect and control. You can use several of these chips. Change A0, A1, A2 pins (if on the same I2C bus) or connect them to a different I2C bus.
Also, if you dont need all the interfaces, most of the CPU pins can be used as GPIO. Check the iMX6 Rex module schematic.